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<li class="navelem"><a class="el" href="dir_bc4a239385bd2ceeb0f261c69ca3e796.html">cudaaligner</a></li><li class="navelem"><a class="el" href="dir_5b3882c99f9a196a3d557147d3c04ffd.html">include</a></li><li class="navelem"><a class="el" href="dir_e25067817972d6e3bb7efd580b3302c4.html">claragenomics</a></li><li class="navelem"><a class="el" href="dir_899653196ec72b3f195a12edb53c5821.html">cudaaligner</a></li>  </ul>
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<div class="title">alignment.hpp</div>  </div>
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<div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="comment">/*</span></div>
<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment">* Copyright (c) 2019, NVIDIA CORPORATION.  All rights reserved.</span></div>
<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment">*</span></div>
<div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="comment">* NVIDIA CORPORATION and its licensors retain all intellectual property</span></div>
<div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="comment">* and proprietary rights in and to this software, related documentation</span></div>
<div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;<span class="comment">* and any modifications thereto.  Any use, reproduction, disclosure or</span></div>
<div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<span class="comment">* distribution of this software and related documentation without an express</span></div>
<div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;<span class="comment">* license agreement from NVIDIA CORPORATION is strictly prohibited.</span></div>
<div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;<span class="comment">*/</span></div>
<div class="line"><a name="l00010"></a><span class="lineno">   10</span>&#160; </div>
<div class="line"><a name="l00011"></a><span class="lineno">   11</span>&#160;<span class="preprocessor">#pragma once</span></div>
<div class="line"><a name="l00012"></a><span class="lineno">   12</span>&#160; </div>
<div class="line"><a name="l00013"></a><span class="lineno">   13</span>&#160;<span class="preprocessor">#include &lt;claragenomics/cudaaligner/cudaaligner.hpp&gt;</span></div>
<div class="line"><a name="l00014"></a><span class="lineno">   14</span>&#160; </div>
<div class="line"><a name="l00015"></a><span class="lineno">   15</span>&#160;<span class="preprocessor">#include &lt;memory&gt;</span></div>
<div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160;<span class="preprocessor">#include &lt;vector&gt;</span></div>
<div class="line"><a name="l00017"></a><span class="lineno">   17</span>&#160;<span class="preprocessor">#include &lt;string&gt;</span></div>
<div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160; </div>
<div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160;<span class="keyword">namespace </span>claragenomics</div>
<div class="line"><a name="l00020"></a><span class="lineno">   20</span>&#160;{</div>
<div class="line"><a name="l00021"></a><span class="lineno">   21</span>&#160; </div>
<div class="line"><a name="l00022"></a><span class="lineno">   22</span>&#160;<span class="keyword">namespace </span>cudaaligner</div>
<div class="line"><a name="l00023"></a><span class="lineno">   23</span>&#160;{</div>
<div class="line"><a name="l00026"></a><span class="lineno">   26</span>&#160; </div>
<div class="line"><a name="l00031"></a><span class="lineno"><a class="line" href="group__cudaaligner.html#ga228dcdd4bf0cf40c64786cce6b045c40">   31</a></span>&#160;<span class="keyword">typedef</span> std::pair&lt;std::string, std::string&gt; <a class="code" href="group__cudaaligner.html#ga228dcdd4bf0cf40c64786cce6b045c40">FormattedAlignment</a>;</div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160; </div>
<div class="line"><a name="l00034"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html">   34</a></span>&#160;<span class="keyword">class </span><a class="code" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html">Alignment</a></div>
<div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;{</div>
<div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;    <span class="keyword">virtual</span> <a class="code" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a6479df67f21d643782abfed873218ea8">~Alignment</a>() = <span class="keywordflow">default</span>;</div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160; </div>
<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;    <span class="keyword">virtual</span> <span class="keyword">const</span> std::string&amp; <a class="code" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#ab29dceafccd3cb0a2e87023c5d48a780">get_query_sequence</a>() <span class="keyword">const</span> = 0;</div>
<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160; </div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;    <span class="keyword">virtual</span> <span class="keyword">const</span> std::string&amp; <a class="code" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a4a61cdee74c32930f49cb878fc17db57">get_target_sequence</a>() <span class="keyword">const</span> = 0;</div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160; </div>
<div class="line"><a name="l00051"></a><span class="lineno">   51</span>&#160;    <span class="keyword">virtual</span> std::string <a class="code" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#aeb4a583f6fbc643c93170797ca45a876">convert_to_cigar</a>() <span class="keyword">const</span> = 0;</div>
<div class="line"><a name="l00052"></a><span class="lineno">   52</span>&#160; </div>
<div class="line"><a name="l00056"></a><span class="lineno">   56</span>&#160;    <span class="keyword">virtual</span> <a class="code" href="group__cudaaligner.html#gafcccbe51c86f9772ccf837fc433f518b">AlignmentType</a> <a class="code" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#ab22457c02ac00ec205dcd5a75b253881">get_alignment_type</a>() <span class="keyword">const</span> = 0;</div>
<div class="line"><a name="l00057"></a><span class="lineno">   57</span>&#160; </div>
<div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160;    <span class="keyword">virtual</span> <a class="code" href="group__cudaaligner.html#ga7d6424e11f69650b1d4eabef0cf4f602">StatusType</a> <a class="code" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a7665f284b7929998357c89461e444f78">get_status</a>() <span class="keyword">const</span> = 0;</div>
<div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160; </div>
<div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;    <span class="keyword">virtual</span> <span class="keyword">const</span> std::vector&lt;AlignmentState&gt;&amp; <a class="code" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a5139f26517193e077000dcddfbc15f70">get_alignment</a>() <span class="keyword">const</span> = 0;</div>
<div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160; </div>
<div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;    <span class="keyword">virtual</span> <a class="code" href="group__cudaaligner.html#ga228dcdd4bf0cf40c64786cce6b045c40">FormattedAlignment</a> <a class="code" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a4be4bb544d593f3fd7624628f2bda29c">format_alignment</a>() <span class="keyword">const</span> = 0;</div>
<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;};</div>
<div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160; </div>
<div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;} <span class="comment">// namespace cudaaligner</span></div>
<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;} <span class="comment">// namespace claragenomics</span></div>
</div><!-- fragment --></div><!-- contents -->
<div class="ttc" id="aclassclaragenomics_1_1cudaaligner_1_1Alignment_html_a7665f284b7929998357c89461e444f78"><div class="ttname"><a href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a7665f284b7929998357c89461e444f78">claragenomics::cudaaligner::Alignment::get_status</a></div><div class="ttdeci">virtual StatusType get_status() const =0</div><div class="ttdoc">Return status of alignment.</div></div>
<div class="ttc" id="agroup__cudaaligner_html_ga228dcdd4bf0cf40c64786cce6b045c40"><div class="ttname"><a href="group__cudaaligner.html#ga228dcdd4bf0cf40c64786cce6b045c40">claragenomics::cudaaligner::FormattedAlignment</a></div><div class="ttdeci">std::pair&lt; std::string, std::string &gt; FormattedAlignment</div><div class="ttdef"><b>Definition:</b> alignment.hpp:31</div></div>
<div class="ttc" id="aclassclaragenomics_1_1cudaaligner_1_1Alignment_html_a4be4bb544d593f3fd7624628f2bda29c"><div class="ttname"><a href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a4be4bb544d593f3fd7624628f2bda29c">claragenomics::cudaaligner::Alignment::format_alignment</a></div><div class="ttdeci">virtual FormattedAlignment format_alignment() const =0</div><div class="ttdoc">Print formatted alignment to stderr.</div></div>
<div class="ttc" id="aclassclaragenomics_1_1cudaaligner_1_1Alignment_html_ab22457c02ac00ec205dcd5a75b253881"><div class="ttname"><a href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#ab22457c02ac00ec205dcd5a75b253881">claragenomics::cudaaligner::Alignment::get_alignment_type</a></div><div class="ttdeci">virtual AlignmentType get_alignment_type() const =0</div><div class="ttdoc">Returns type of alignment.</div></div>
<div class="ttc" id="aclassclaragenomics_1_1cudaaligner_1_1Alignment_html_a5139f26517193e077000dcddfbc15f70"><div class="ttname"><a href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a5139f26517193e077000dcddfbc15f70">claragenomics::cudaaligner::Alignment::get_alignment</a></div><div class="ttdeci">virtual const std::vector&lt; AlignmentState &gt; &amp; get_alignment() const =0</div><div class="ttdoc">Get the alignment between sequences.</div></div>
<div class="ttc" id="aclassclaragenomics_1_1cudaaligner_1_1Alignment_html_aeb4a583f6fbc643c93170797ca45a876"><div class="ttname"><a href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#aeb4a583f6fbc643c93170797ca45a876">claragenomics::cudaaligner::Alignment::convert_to_cigar</a></div><div class="ttdeci">virtual std::string convert_to_cigar() const =0</div><div class="ttdoc">Converts an alignment to CIGAR format. The is a reduced implementation of the CIGAR standard supporti...</div></div>
<div class="ttc" id="aclassclaragenomics_1_1cudaaligner_1_1Alignment_html"><div class="ttname"><a href="classclaragenomics_1_1cudaaligner_1_1Alignment.html">claragenomics::cudaaligner::Alignment</a></div><div class="ttdoc">Alignment - Object encapsulating an alignment between 2 string.</div><div class="ttdef"><b>Definition:</b> alignment.hpp:34</div></div>
<div class="ttc" id="aclassclaragenomics_1_1cudaaligner_1_1Alignment_html_a6479df67f21d643782abfed873218ea8"><div class="ttname"><a href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a6479df67f21d643782abfed873218ea8">claragenomics::cudaaligner::Alignment::~Alignment</a></div><div class="ttdeci">virtual ~Alignment()=default</div><div class="ttdoc">Virtual destructor.</div></div>
<div class="ttc" id="aclassclaragenomics_1_1cudaaligner_1_1Alignment_html_ab29dceafccd3cb0a2e87023c5d48a780"><div class="ttname"><a href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#ab29dceafccd3cb0a2e87023c5d48a780">claragenomics::cudaaligner::Alignment::get_query_sequence</a></div><div class="ttdeci">virtual const std::string &amp; get_query_sequence() const =0</div><div class="ttdoc">Returns query sequence.</div></div>
<div class="ttc" id="agroup__cudaaligner_html_gafcccbe51c86f9772ccf837fc433f518b"><div class="ttname"><a href="group__cudaaligner.html#gafcccbe51c86f9772ccf837fc433f518b">claragenomics::cudaaligner::AlignmentType</a></div><div class="ttdeci">AlignmentType</div><div class="ttdoc">AlignmentType - Enum for storing type of alignment.</div><div class="ttdef"><b>Definition:</b> cudaaligner.hpp:36</div></div>
<div class="ttc" id="agroup__cudaaligner_html_ga7d6424e11f69650b1d4eabef0cf4f602"><div class="ttname"><a href="group__cudaaligner.html#ga7d6424e11f69650b1d4eabef0cf4f602">claragenomics::cudaaligner::StatusType</a></div><div class="ttdeci">StatusType</div><div class="ttdoc">CUDA Aligner error type.</div><div class="ttdef"><b>Definition:</b> cudaaligner.hpp:25</div></div>
<div class="ttc" id="aclassclaragenomics_1_1cudaaligner_1_1Alignment_html_a4a61cdee74c32930f49cb878fc17db57"><div class="ttname"><a href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a4a61cdee74c32930f49cb878fc17db57">claragenomics::cudaaligner::Alignment::get_target_sequence</a></div><div class="ttdeci">virtual const std::string &amp; get_target_sequence() const =0</div><div class="ttdoc">Returns target sequence.</div></div>
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